diff --git a/.gitignore b/.gitignore
index 3cb3963..3bbfb9d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,3 +5,7 @@ dist
testfiles
target
lib
+.settings
+src/log4j.properties
+.project
+.classpath
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
index 4eaaa66..ba08d03 100644
--- a/pom.xml
+++ b/pom.xml
@@ -3,7 +3,7 @@
de.unirostock.sems
BiVeS
jar
- 1.9.2
+ 1.10.0
BiVeS
BiVeS - BioModel Version Control System
@@ -36,17 +36,17 @@
de.unirostock.sems
BiVeS-SBML
- 1.7.5
+ 1.8.0
de.unirostock.sems
BiVeS-CellML
- 1.6.6
+ 1.7.1
de.unirostock.sems
BiVeS-Core
- 1.7.2
+ 1.8.1
commons-cli
@@ -58,6 +58,12 @@
log4j
1.2.17
+
+ de.unirostock.sems
+ BiVeS
+ 1.9.1
+ provided
+
http://mvn.sems.uni-rostock.de
diff --git a/src/main/java/de/unirostock/sems/bives/Executer.java b/src/main/java/de/unirostock/sems/bives/Executer.java
index 3b329fb..012b147 100644
--- a/src/main/java/de/unirostock/sems/bives/Executer.java
+++ b/src/main/java/de/unirostock/sems/bives/Executer.java
@@ -81,6 +81,9 @@ public class Executer
public static final String REQ_WANT_REACTIONS_DOT = "reactionsDot";
public static final String REQ_WANT_REACTIONS_DOT2 = "crnDot";
+ /** The Constant REQ_WANT_REACTIONS_SBGN_JSON. */
+ public static final String REQ_WANT_REACTIONS_SBGN_JSON = "reactionsSbgnJson";
+
/** The Constant REQ_WANT_REACTIONS_JSON. */
public static final String REQ_WANT_REACTIONS_JSON = "reactionsJson";
public static final String REQ_WANT_REACTIONS_JSON2 = "crnJson";
@@ -188,6 +191,7 @@ private void fillOptions ()
options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_GRAPHML).desc ("get the highlighted reaction network encoded in GraphML").build ());
options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_DOT).desc ("get the highlighted reaction network encoded in DOT language").build ());
options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_JSON).desc ("get the highlighted reaction network encoded in JSON").build ());
+ options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_SBGN_JSON).desc ("get the highlighted reaction network encoded in an SBGN-JSON format").build ());
options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_GRAPHML2).desc ("get the highlighted reaction network encoded in GraphML (deprecated version)").build ());
options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_DOT2).desc ("get the highlighted reaction network encoded in DOT language (deprecated version)").build ());
options.addOption (Option.builder ().longOpt (REQ_WANT_REACTIONS_JSON2).desc ("get the highlighted reaction network encoded in JSON (deprecated version)").build ());
@@ -509,6 +513,17 @@ else if ((type & DocumentClassifier.XML) != 0)
errors.add (e);
}
+ if (line.hasOption (REQ_WANT_REACTIONS_SBGN_JSON))
+ try
+ {
+ hasOption = true;
+ toReturn.put (Executer.REQ_WANT_REACTIONS_SBGN_JSON, result (diff.getReactionsSbgnJsonGraph ()));
+ }
+ catch (Exception e)
+ {
+ errors.add (e);
+ }
+
if (line.hasOption (REQ_WANT_COMP_HIERARCHY_DOT))
try
{